Confirming for webpages as well: Looking at them with userstyle revealing transcripts [1], last comic with proper transcript was Hoverboard #1608, next two have their empty but in fact they appears shifted as described by OP. I.e. transcript for Food Combinations #1609 appears below Baking Soda and Vinegar #1611.

transcriptComic will be the comic with the correct transcript. Also note that comics after 1678 (inclusive) do not have transcripts (yet) and transcriptComic could be a comic that doesn't exist.

This means that (until this is fixed) comics 1608 (Hoverboard) and 1663 (Garden) do not have transcripts and are messing up all the other transcripts. These are the two interactive comics that are wierd, which is probably why it is broken.